Updated restraint dictionaries for carbohydrates in the pyranose form

Atanasova, M.; Nicholls, R.A.; Joosten, R.P.; Agirre, J.

doi:10.1107/S2059798322001103

Acta Crystallographica Section D
Acta Crystallographica
Section D STRUCTURAL BIOLOGY

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Figure 6
Change in conformation and real-space correlation coefficient (RSCC) after refinement. (a) Sugar in a ¹S₅ conformation after refinement with its old CCP4-ML restraint dictionary entry (Fig. 4

a, bottom middle panel). (b) The conformation of the sugar has been changed to the minimal energy conformation after refinement with the updated restraint dictionary entry and unimodal torsion restraints and the RSCC has increased (Fig. 4

a, top middle panel). The sugar in (a) and (b) is MAN-Q-4 from PDB entry 4uo0 (Devi et al., 2015

) at 1.90 Å resolution, mean B value 34 Å². (c) Sugar in a ²S_O conformation after refinement with its old CCP4-ML restraint dictionary entry (Fig. 4

a, bottom middle panel). (d) The minimal energy conformation of the sugar after refinement with the new restraint dictionary entry and unimodal torsion restraints; the RSCC has decreased (Fig. 4

a, top middle panel). The sugar in (c) and (d) is BMA-P-3 from PDB entry 4iic (Suzuki et al., 2013

) at 1.90 Å resolution, mean B value 18 Å². This figure was produced with CCP4mg (McNicholas et al., 2011

). Maps are displayed at a 1σ contour level with a sampling rate of 0.5.

STRUCTURAL
BIOLOGY

ISSN: 2059-7983

Volume 78| Part 4| April 2022| Pages 455-465

https://doi.org/10.1107/S2059798322001103

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